Regarding the sound problems on SNES9x GX v0.0.4x and v0.0.5x, I tried playing Mortal Kombat II on SNES9x v1.43 on my computer and the game played fine without any of the long distorted sound problems. So, the sound for MKII plays just fine on SNES9x v1.43 on the computer but when I try to play the game on the Gamecube using SNES9xGX the game has sound problems.
I imagine that the case above is probably similar for all of the other games i've played that have the bizarre distorted sound problems on SNES9xGX, including Road Runner's Death Valley Rally, Secret of Evermore, and Ultimate Mortal Kombat 3. One game that has sound issues on both types of emulators though is Earthworm Jim 2, or is it part 1? I'm thinking part 2. Although i remember that every SNES emulator that plays SNES games has trouble emulating the sound in Earthworm Jim 2.